1O9I

CRYSTAL STRUCTURE OF THE Y42F MUTANT OF MANGANESE CATALASE FROM LACTOBACILLUS PLANTARUM AT 1.33A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.115 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Outer Sphere Mutagenesis of Lactobacillus Plantarum Manganese Catalase Disrupts the Cluster Core. Mechanistic Implications.

Whittaker, M.M.Barynin, V.V.Igarashi, T.Whittaker, J.W.

(2003) Eur.J.Biochem. 270: 1102


  • PubMed Abstract: 
  • X-ray crystallography of the nonheme manganese catalase from Lactobacillus plantarum (LPC) [Barynin, V.V., Whittaker, M.M., Antonyuk, S.V., Lamzin, V.S., Harrison, P.M., Artymiuk, P.J. & Whittaker, J.W. (2001) Structure9, 725-738] has revealed the st ...

    X-ray crystallography of the nonheme manganese catalase from Lactobacillus plantarum (LPC) [Barynin, V.V., Whittaker, M.M., Antonyuk, S.V., Lamzin, V.S., Harrison, P.M., Artymiuk, P.J. & Whittaker, J.W. (2001) Structure9, 725-738] has revealed the structure of the dimanganese redox cluster together with its protein environment. The oxidized [Mn(III)Mn(III)] cluster is bridged by two solvent molecules (oxo and hydroxo, respectively) together with a micro 1,3 bridging glutamate carboxylate and is embedded in a web of hydrogen bonds involving an outer sphere tyrosine residue (Tyr42). A novel homologous expression system has been developed for production of active recombinant LPC and Tyr42 has been replaced by phenylalanine using site-directed mutagenesis. Spectroscopic and structural studies indicate that disruption of the hydrogen-bonded web significantly perturbs the active site in Y42F LPC, breaking one of the solvent bridges and generating an 'open' form of the dimanganese cluster. Two of the metal ligands adopt alternate conformations in the crystal structure, both conformers having a broken solvent bridge in the dimanganese core. The oxidized Y42F LPC exhibits strong optical absorption characteristic of high spin Mn(III) in low symmetry and lower coordination number. MCD and EPR measurements provide complementary information defining a ferromagnetically coupled electronic ground state for a cluster containing a single solvent bridge, in contrast to the diamagnetic ground state found for the native cluster containing a pair of solvent bridges. Y42F LPC has less than 5% of the catalase activity and much higher Km for H2O2 ( approximately 1.4 m) at neutral pH than WT LPC, although the activity is slightly restored at high pH where the cluster is converted to a diamagnetic form. These studies provide new insight into the contribution of the outer sphere tyrosine to the stability of the dimanganese cluster and the role of the solvent bridges in catalysis by dimanganese catalases.


    Related Citations: 
    • Crystal Structure of Manganese Catalase from Lactobacillus Plantarum
      Barynin, V.V.,Whittaker, M.M.,Antonyuk, S.V.,Lamzin, V.S.,Harrison, P.M.,Artymiuk, P.J.,Whittaker, J.W.
      (2001) Structure 9: 725


    Organizational Affiliation

    Department of Environmental and Biomolecular Systems, OGI School of Science and Engineering at OHSU, Oregon, USA. jim@bmb.ogi.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PSEUDOCATALASE
A, B, C, D, E, F
266Lactobacillus plantarumEC: 1.11.1.6
Find proteins for P60355 (Lactobacillus plantarum)
Go to UniProtKB:  P60355
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A, B, C, D, E, F
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MN3
Query on MN3

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A, B, C, D, E, F
MANGANESE (III) ION
Mn
MMIPFLVOWGHZQD-UHFFFAOYSA-N
 Ligand Interaction
O
Query on O

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A, B, C, D, E, F
OXYGEN ATOM
O
XLYOFNOQVPJJNP-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

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A, E, F
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.115 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 73.490α = 90.00
b = 95.270β = 106.55
c = 105.000γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-12-18
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance